{ "_id": "6a0f637bacfb0bcc41c5c842", "Package": "denvax", "Type": "Package", "Title": "Simple Dengue Test and Vaccinate Cost Thresholds", "Version": "0.1.3", "Authors@R": "c(\nperson(\"Carl A. B.\", \"Pearson\", email=\"carl.pearson@lshtm.ac.uk\", role = c(\"aut\",\"cre\"), comment = c(ORCID=\"0000-0003-0701-7860\")),\nperson(\"Kaja M.\", \"Abbas\", role = c(\"aut\"), comment = c(ORCID=\"0000-0003-0563-1576\")),\nperson(\"Samuel\", \"Clifford\", role = c(\"aut\"), comment = c(ORCID=\"0000-0002-3774-3882\")),\nperson(\"Stefan\", \"Flasche\", role = c(\"aut\"), comment = c(ORCID=\"0000-0002-5808-2606\")),\nperson(\"Thomas J.\", \"Hladish\", role = c(\"aut\"), comment = c(ORCID=\"0000-0003-1819-6235\"))\n)", "Description": "Provides the mathematical model described by \"Serostatus\nTesting & Dengue Vaccine Cost-Benefit Thresholds\" in\n. Using the functions in the\npackage, that analysis can be repeated using sample life\nhistories, either synthesized from local seroprevalence data\nusing other functions in this package (as in the manuscript) or\nfrom some other source. The package provides a vignette which\nwalks through the analysis in the publication, a function to\ngenerate a project skeleton for such an analysis, and a shiny\napp to run scenarios.", "License": "MIT + file LICENSE", "Encoding": "UTF-8", "LazyData": "true", "RoxygenNote": "7.0.2", "VignetteBuilder": "knitr", "URL": "https://gitlab.com/cabp_LSHTM/denvax", "BugReports": "https://gitlab.com/cabp_LSHTM/denvax/issues", "Repository": "https://pearsonca.r-universe.dev", "Date/Publication": "2020-02-28 07:49:04 UTC", "RemoteUrl": "https://gitlab.com/cabp_lshtm/denvax", "RemoteRef": "HEAD", "RemoteSha": "02a18792abd3f42c662a9c190b169898210224ce", "NeedsCompilation": "no", "Packaged": { "Date": "2026-05-21 10:30:04 UTC", "User": "root" }, "Author": "Carl A. B. Pearson [aut, cre] (ORCID:\n),\nKaja M. Abbas [aut] (ORCID: ),\nSamuel Clifford [aut] (ORCID: ),\nStefan Flasche [aut] (ORCID: ),\nThomas J. Hladish [aut] (ORCID:\n)", "Maintainer": "Carl A. B. Pearson ", "MD5sum": "fa893d25a71a113781f3b0ef135fde2b", "_user": "pearsonca", "_type": "src", "_file": "denvax_0.1.3.tar.gz", "_fileid": "1f319b85545116888b04a99a84e69032b91214ecf068e9f264bfc4c51ea78e00", "_filesize": 182517, "_sha256": "1f319b85545116888b04a99a84e69032b91214ecf068e9f264bfc4c51ea78e00", "_created": "2026-05-21T10:30:04.000Z", "_published": "2026-05-21T19:56:43.796Z", "_distro": "noble", "_jobs": [ { "job": 77256886351, "time": 160, "config": "linux-devel-x86_64", "r": "4.7.0", "check": "NOTE", "artifact": "7133433978" }, { "job": 77256886376, "time": 163, "config": "linux-release-x86_64", "r": "4.6.0", "check": "NOTE", "artifact": "7133435137" }, { "job": 77256886826, "time": 193, "config": "macos-oldrel-arm64", "r": "4.5.3", "check": "NOTE", "artifact": "7133436743" }, { "job": 77256886662, "time": 152, "config": "macos-release-arm64", "r": "4.6.0", "check": "NOTE", "artifact": "7133425352" }, { "job": 77256885954, "time": 165, "config": "source", "r": "4.6.0", "check": "OK", "artifact": "7133382493" }, { "job": 77256885938, "time": 115, "config": "wasm-release", "r": "4.6.0", "check": "OK", "artifact": "7145815337" }, { "job": 77256886453, "time": 116, "config": "windows-devel", "r": "4.7.0", "check": "NOTE", "artifact": "7133420499" }, { "job": 77256886886, "time": 86, "config": "windows-oldrel", "r": "4.5.3", "check": "NOTE", "artifact": "7133411289" }, { "job": 77256886885, "time": 86, "config": "windows-release", "r": "4.6.0", "check": "NOTE", "artifact": "7133411132" } ], "_buildurl": "https://github.com/r-universe/pearsonca/actions/runs/26220390926", "_status": "success", "_host": "GitHub-Actions", "_upstream": "https://gitlab.com/cabp_lshtm/denvax", "_commit": { "id": "02a18792abd3f42c662a9c190b169898210224ce", "author": "Carl A. B. Pearson ", "committer": "Carl A. B. Pearson ", "message": "final tweaks for LSHTM RUG demo\n", "time": 1582876144 }, "_maintainer": { "name": "Carl A. B. Pearson", "email": "carl.pearson@lshtm.ac.uk", "login": "pearsonca", "orcid": "0000-0003-0701-7860", "description": "STEM researcher.", "uuid": 1828039 }, "_registered": true, "_dependencies": [ { "package": "R", "version": ">= 3.5", "role": "Depends" }, { "package": "data.table", "role": "Suggests" }, { "package": "ggplot2", "role": "Suggests" }, { "package": "shiny", "role": "Suggests" }, { "package": "renv", "role": "Suggests" }, { "package": "testthat", "role": "Suggests" }, { "package": "usethis", "role": "Suggests" }, { "package": "devtools", "role": "Suggests" }, { "package": "roxygen2", "role": "Suggests" }, { "package": "rmarkdown", "role": "Suggests" }, { "package": "knitr", "role": "Suggests" }, { "package": "cowplot", "role": "Suggests" }, { "package": "jsonlite", "role": "Suggests" }, { "package": "directlabels", "role": "Suggests" } ], "_owner": "gitlab-cabp_lshtm", "_selfowned": true, "_usedby": 0, "_updates": [], "_tags": [], "_userbio": { "uuid": 1828039, "type": "user", "name": "Carl A. B. Pearson", "description": "STEM researcher." }, "_downloads": { "count": 207, "source": "https://cranlogs.r-pkg.org/downloads/total/last-month/denvax" }, "_mentions": 1, "_devurl": "https://gitlab.com/cabp_lshtm/denvax", "_searchresults": 1, "_rbuild": "4.6.0", "_assets": [ "extra/citation.cff", "extra/citation.html", "extra/citation.json", "extra/citation.txt", "extra/contents.json", "extra/denvax.html", "extra/readme.html", "extra/readme.md", "manual.pdf" ], "_homeurl": "https://gitlab.com/cabp_lshtm/denvax", "_realowner": "pearsonca", "_cranurl": true, "_releases": [ { "version": "0.1.0", "date": "2019-07-19" }, { "version": "0.1.1", "date": "2019-08-21" }, { "version": "0.1.2", "date": "2019-12-01" } ], "_exports": [ "build.project", "denvaxApp", "nPxA", "rescale_x_Tcost", "rescale_y_Vcost", "ROI", "ROIcoeffs", "scale_color_ROIsign", "scale_fill_ROI", "scale_linetype_ROIlvl", "scale_x_log10tau", "scale_x_startAge", "scale_y_endAge", "scale_y_nu", "scale_y_numTests", "serofit", "synthetic.pop" ], "_datasets": [ { "name": "lazou2016", "title": "The serosurvey data in L'Azou 2016", "object": "lazou2016", "class": [ "data.table", "data.frame" ], "fields": [ "Country", "Age", "Number", "Seropositive" ], "rows": 20, "table": true, "tojson": true }, { "name": "morrison2010", "title": "The serosurvey data in Morrison 2010", "object": "morrison2010", "class": [ "data.table", "data.frame" ], "fields": [ "Country", "Age", "Number", "Seropositive" ], "rows": 13, "table": true, "tojson": true } ], "_help": [ { "page": "build.project", "title": "Creates an ROI estimation project.", "topics": [ "build.project" ] }, { "page": "denvax", "title": "denvax: Simple Dengue Test and Vaccinate Cost Thresholds", "topics": [ "denvax" ] }, { "page": "denvax_scales", "title": "Provide customized ggplot2 continuous scales", "topics": [ "denvax_scales", "rescale_x_Tcost", "rescale_y_Vcost", "scale_color_ROIsign", "scale_fill_ROI", "scale_linetype_ROIlvl", "scale_x_log10tau", "scale_x_startAge", "scale_y_endAge", "scale_y_nu", "scale_y_numTests" ] }, { "page": "denvaxApp", "title": "Launches shiny apps for denvax analyses.", "topics": [ "denvaxApp" ] }, { "page": "lazou2016", "title": "The serosurvey data in L'Azou 2016", "topics": [ "lazou2016" ] }, { "page": "morrison2010", "title": "The serosurvey data in Morrison 2010", "topics": [ "morrison2010" ] }, { "page": "nPxA", "title": "Compute the nPx(A), C(A) proportions from a population of life histories", "topics": [ "nPxA" ] }, { "page": "ROI", "title": "Compute the ROI surfaces given test and vaccine cost fractions.", "topics": [ "ROI" ] }, { "page": "ROIcoeffs", "title": "Compute the Return on Investment (ROI) surface coefficients from population probabilities", "topics": [ "ROIcoeffs" ] }, { "page": "serofit", "title": "Model fitting for serological data", "topics": [ "serofit" ] }, { "page": "synthetic.pop", "title": "Compute synthetic population trajectories from model parameters", "topics": [ "synthetic.pop" ] } ], "_readme": "https://gitlab.com/cabp_lshtm/denvax/raw/HEAD/README.md", "_rundeps": [], "_vignettes": [ { "source": "published-analysis.Rmd", "filename": "published-analysis.html", "title": "Published Test-then-Vaccinate ROI Analyses", "engine": "knitr::rmarkdown", "headings": [], "created": "2019-05-05 11:14:24", "modified": "2019-08-21 07:36:41", "commits": 13 } ], "_score": 3.6989700043360187, "_indexed": true, "_nocasepkg": "denvax", "_universes": [ "pearsonca", "gitlab-cabp_lshtm" ], "_binaries": [ { "r": "4.7.0", "os": "linux", "version": "0.1.3", "date": "2026-05-21T10:32:30.000Z", "distro": "noble", "commit": "02a18792abd3f42c662a9c190b169898210224ce", "fileid": "863ed1fd77d8d6b99cd19508f112c5abf34a45ca88b37b75c777aa4eb111c045", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/pearsonca/actions/runs/26220390926" }, { "r": "4.6.0", "os": "linux", "version": "0.1.3", "date": "2026-05-21T10:32:38.000Z", "distro": "noble", "commit": "02a18792abd3f42c662a9c190b169898210224ce", "fileid": "95b2f736834dc20f88db147fcbd7fdbda1d91857a5da471c34e8ff9f917c7577", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/pearsonca/actions/runs/26220390926" }, { "r": "4.5.3", "os": "mac", "version": "0.1.3", "date": "2026-05-21T10:32:47.000Z", "commit": "02a18792abd3f42c662a9c190b169898210224ce", "fileid": "57b53f0f59ff45d5ec453e8a9521516465d7fad0ced105b9c556643214151db2", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/pearsonca/actions/runs/26220390926" }, { "r": "4.6.0", "os": "mac", "version": "0.1.3", "date": "2026-05-21T10:32:12.000Z", "commit": "02a18792abd3f42c662a9c190b169898210224ce", "fileid": "2d8e2e988ca749e6d878f3721d7d26f0cbf0d686f495d43301cfe716769b7b77", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/pearsonca/actions/runs/26220390926" }, { "r": "4.6.0", "os": "wasm", "version": "0.1.3", "date": "2026-05-21T19:56:22.000Z", "commit": "02a18792abd3f42c662a9c190b169898210224ce", "fileid": "43a45df17908bd85e63284be51760561da4988177a0b3b4dce150e2651950ded", "status": "success", "buildurl": "https://github.com/r-universe/pearsonca/actions/runs/26220390926" }, { "r": "4.7.0", "os": "win", "version": "0.1.3", "date": "2026-05-21T10:31:46.000Z", "commit": "02a18792abd3f42c662a9c190b169898210224ce", "fileid": "f85fd2abdd8aa08d3d7b4fb1bf1108553a7a6ffda72918b823ea1c5c99df4feb", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/pearsonca/actions/runs/26220390926" }, { "r": "4.5.3", "os": "win", "version": "0.1.3", "date": "2026-05-21T10:31:17.000Z", "commit": "02a18792abd3f42c662a9c190b169898210224ce", "fileid": "4977fcce399be9ad48c99354fc3a1d242b6b21b03837311dfecb96a9b11889f7", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/pearsonca/actions/runs/26220390926" }, { "r": "4.6.0", "os": "win", "version": "0.1.3", "date": "2026-05-21T10:31:15.000Z", "commit": "02a18792abd3f42c662a9c190b169898210224ce", "fileid": "eb1998e2c9a5cba72a3c3f79f249b32022d374cf2ff4e537f9813774bdd40730", "status": "success", "check": "NOTE", "buildurl": "https://github.com/r-universe/pearsonca/actions/runs/26220390926" } ] }